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OnderzoekZernike (ZIAM)

Refereed academic publications of 1996

Molecular Dynamics
  1. Amadei, A., Linssen, A.B.M., de Groot, B.L., van Aalten, D.M.F. & Berendsen, H.J.C. An efficient method for sampling the essential subspace of proteins. Journal of Biomolecular Structure & Dynamics 13 (4) 615-625 (1996)

  2. Amadei, A., Roccatano, D., Apol, M.E.F., Berendsen, H.J.C. & Di Nola, A. Prediction of the liquid-vapor equilibrium pressure using the quasi-Gaussian entropy theory. Journal of Chemical Physics 105 (16) 7022-7025 (1996)

  3. Amadei, A., Apol, M.E.F., Di Nola, A. & Berendsen, H.J.C. The quasi-Gaussian entropy theory: Free energy calculations based on the potential energy distribution function. Journal of Chemical Physics 104 (4) 1560-1574 (1996)

  4. Apol, M.E.F., Amadei, A. & Berendsen, H.J.C. Application of the quasi-Gaussian entropy theory to the calculation of thermodynamic properties of water and methane in the liquid and gas phase. Journal of Chemical Physics 104 (17) 6665-6678 (1996)

  5. Apol, M.E.F., Amadei, A. & Berendsen, H.J.C. Derivation of a thermodynamic closure relation in the isothermal-isobaric ensemble using quasi-Gaussian entropy theory. Chemical Physics Letters 256 (1-2) 172-178 (1996)

  6. Berendsen, H.J.C. & Mavri, J. Approach to nonadiabatic transitions by density matrix evolution and molecular dynamics simulations. International Journal of Quantum Chemistry 57 (5) 975-983 (1996)

  7. Berendsen, H.J.C. Bio-molecular dynamics comes of age. Science 271 (5251) 954-955 (1996)

  8. Cascales, J.J.L., Berendsen, H.J.C. & delaTorre, J.G. Molecular dynamics simulation of water between two charged layers of dipalmitoylphosphatidylserine. Journal of Physical Chemistry 100 (21) 8621-8627 (1996)

  9. Cascales, J.J.L., delaTorre, J.G., Marrink, S.J. & Berendsen, H.J.C. Molecular dynamics simulation of a charged biological membrane. Journal of Chemical Physics 104 (7) 2713-2720 (1996)

  10. Daura, X., Hunenberger, P.H., Mark, A.E., Querol, E., Aviles, F.X. & Gunsteren, W.F.v. Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions. Journal of the American Chemical Society 118 (26) 6285-6294 (1996)

  11. de Groot, B.L., Amadei, A., Scheek, R.M., van Nuland, N.A.J. & Berendsen, H.J.C. An extended sampling of the configurational space of HPr from E-coli. Proteins-Structure Function and Genetics 26 (3) 314-322 (1996)

  12. de Groot, B.L., van Aalten, D.M.F., Amadei, A. & Berendsen, H.J.C. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophysical Journal 71 (4) 1707-1713 (1996)

  13. de Groot, B.L., Amadei, A., van Aalten, D.M.F. & Berendsen, H.J.C. Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. Journal of Biomolecular Structure & Dynamics 13 (5) 741-751 (1996)

  14. de Wijs, G.A., Pastore, G., Selloni, A. & van der Lugt, W. First-principles molecular dynamics simulation of liquid Mg3Bi2. Journal of Physics-Condensed Matter 8 (12) 1879-1896 (1996)

  15. Fraaije, J.G.E.M. & van Vlimmeren, B.A.C. The study of biomembrane assembly dynamics using combined mesoscopic and microscopic free energy models. Biophysical Journal 70 (2) TUP10 (1996)

  16. Hess, B. & Fraaije, J.G.E.M. A field description of proteins. Progress in Biophysics & Molecular Biology 65 A426 (1996)

  17. Lensink, M.F., Mavri, J. & Berendsen, H.J.C. Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integrator. Journal of Computational Chemistry 17 (11) 1287-1295 (1996)

  18. Lijnzaad, P., Berendsen, H.J.C. & Argos, P. A method for detecting hydrophobic patches protein. Proteins-Structure Function and Genetics 26 (2) 192-203 (1996)

  19. Lijnzaad, P., Berendsen, H.J.C. & Argos, P. Hydrophobic patches on the surfaces of protein structures. Proteins-Structure Function and Genetics 25 (3) 389-397 (1996)

  20. Liu, H.Y., Mark, A.E. & Gunsteren, W.F.v. Estimating the relative free energy of different molecular states with respect to a single reference state. Journal of Physical Chemistry 100 (22) 9485-9494 (1996)

  21. Marrink, S.J., Sok, R.M. & Berendsen, H.J.C. Free volume properties of a simulated lipid membrane. Journal of Chemical Physics 104 (22) 9090-9099 (1996)

  22. Marrink, S.J., Tieleman, D.P., van Buuren, A.R. & Berendsen, H.J.C. Membranes and water: An interesting relationship. Faraday Discussions (103) 191-201 (1996)

  23. Marrink, S.J. & Berendsen, H.J.C. Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations. Journal of Physical Chemistry 100 (41) 16729-16738 (1996)

  24. Marrink, S.J., Jahnig, F. & Berendsen, H.J.C. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophysical Journal 71 (2) 632-647 (1996)

  25. Maurits, N.M. & Fraaije, J.G.E.M. Modelling of dynamic mesoscopic processes in biological complex fluids using dynamic density functional methods. Zeitschrift fur Angewandte Mathematik und Mechanik 76 475-476 (1996)

  26. Maurits, N.M., Fraaije, J.G.E.M., Altevogt, P. & Evers, O.A. Simple numerical quadrature rules for Gaussian chain polymer density functional calculations in 3D and implementation on parallel platforms. Computational & Theoretical Polymer Science 6 (1-2) 1-8 (1996)

  27. Tieleman, D.P. & Berendsen, H.J.C. Molecular dynamics simulations of a fully hydrated dipalmitoyl phosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. Journal of Chemical Physics 105 (11) 4871-4880 (1996)

  28. Tieleman, D.P., Lopez, C.J.J. & Berendsen, H.J.C. Molecular dynamics studies of lipids and proteins of the E-coli outer membrane: POPE and OmpF. Progress in Biophysics & Molecular Biology 65 C443 (1996)

  29. van Aalten, D.M.F., Amadei, A., Bywater, R., Findlay, J.B.C., Berendsen, H.J.C., Sander, C. & Stouten, P.F.W. Comparison of structural and dynamic properties of different simulation methods applied to SH3. Biophysical Journal 70 (2) 684-692 (1996)

  30. van Aalten, D.M.F., de Groot, B.L., Berendsen, H.J.C. & Findlay, J.B.C. Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins. Biochemical Journal 319 543-550 (1996)

  31. van Buuren, A.R., Tieleman, D.P., de Vlieg, J. & Berendsen, H.J.C. Cosurfactants lower surface tension of the diglyceride/water interface: A molecular dynamics study. Langmuir 12 (10) 2570-2579 (1996)

  32. van der Spoel, D., de Groot, B.L., Hayward, S., Berendsen, H.J.C. & Vogel, H.J. Bending of the calmodulin central helix: A theoretical study. Protein Science 5 (10) 2044-2053 (1996)

  33. van der Spoel, D., van Buuren, A.R., Tieleman, D.P. & Berendsen, H.J.C. Molecular dynamics simulations of peptides from BPTI: A closer look at amide-aromatic interactions. Journal of Biomolecular Nmr 8 (3) 229-238 (1996)

  34. van der Spoel, D., Vogel, H.J. & Berendsen, H.J.C. Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein. Proteins-Structure Function and Genetics 24 (4) 450-466 (1996)

  35. van der Spoel, D., Feenstra, K.A., Hemminga, M.A. & Berendsen, H.J.C. Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic mottle virus coat protein in solution with phosphate ions. Biophysical Journal 71 (6) 2920-2932 (1996)

  36. van Vlimmeren, B.A.C. & Fraaije, J.G.E.M. Calculation of noise distribution in mesoscopic dynamics models for phase separation of multicomponent complex fluids. Computer Physics Communications 99 (1) 21-28 (1996)

  37. van Vlimmeren, B.A.C., Postma, M., Huetz, P. & Fraaije, J.G.E.M. Computer simulation of mesoscale phenomena: Pattern formation in biomimicking complex fluids. Progress in Biophysics & Molecular Biology 65 D108 (1996)

  38. van Vlimmeren, B.A.C., Postma, M., Huetz, P., Brisson, A. & Fraaije, J.G.E.M. Functional Langevin models for the mesoscopic dynamics of surfactant aggregation in solution. Physical Review E 54 (5) 5836-5839 (1996)

Last modified:22 October 2012 2.29 p.m.